[Eeglablist] [External] Re: Plotting standard error shades on ERP

Dr Cyril, Pernet wamcyril at gmail.com
Wed Jul 21 06:53:14 PDT 2021


with LIMO tools that's never a problem (number of subjects, channels, 
etc .. being different is always handled via bootstrap)

On 21/07/2021 15:05, Beach, Paul wrote:
> Cyril - thanks for the suggestion. I will have to do a lot more 
> reading on LIMO before I try to use it - it’s on the ’to do’ list.
>
> One thing I run into frequently with trying to get standard error 
> shades is "Some conditions have more subjects than others, cannot plot 
> standard error.” Is there a way around this?
>
>
>> On Jul 20, 2021, at 12:44 PM, Dr Cyril, Pernet <wamcyril at gmail.com 
>> <mailto:wamcyril at gmail.com>> wrote:
>>
>> Hi Paul,
>>
>> testing differences is well performed using a hierarchical linear 
>> model accounting for within-subject (between trials), and between 
>> subjects variances - a robust difference (yuen t-test) can be 
>> computed companioned by ERP Highest-density Intervals ; see e.g. 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LIMO-2DEEG-2DToolbox_limo-5Ftools_wiki_Plotting-2Ddifferences&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=Z7xZV5R_nUk8PVGqkl2HGJUdeipDuU0QmiPBEkN30Z4&s=tk3hcaKsYBjTyazV86YZYzfLa0YyoXDt3xquG-dCwz4&e= 
>>
>> cyril
>>
>>
>> <kmimhdjbodokcjmd.png>
>>
>> On 20/07/2021 18:31, Beach, Paul via eeglablist wrote:
>>> Thank you, Arnaud and Cedric for your replies.
>>>
>>> Arnaud - I was able to get it to work using the command line text found in the link you forwarded. I’m wondering, though, how I can modify things to directly test different conditions.
>>>
>>> [STUDY erpdata erptimes] = std_erpplot(STUDY, ALLEEG, 'channels', {'Fp1'}, 'timerange', [-200 800]);
>>> std_plotcurve(erptimes, erpdata, 'plotconditions', 'together', 'plotstderr', 'on', 'figure', 'on', 'filter', 10);
>>>
>>> Right now the above command plots things based on the last design selection I made using the STUDY GUI. Unfortunately making changes in the GUI are not reflected in eegh, so I can’t use that to figure out things myself. Is there a way around this, so I can further learn how to make modifications independent of the GUI?
>>>
>>> Thanks!
>>> --
>>> Paul Beach DO, PhD
>>> PGY6, Movement Disorder Fellow
>>> Department of Neurology
>>> Emory University School of Medicine
>>>
>>> On Jul 19, 2021, at 3:26 PM, Delorme, Arnaud via eeglablist <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>> wrote:
>>>
>>> You can also do that at the study level
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__nam11.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Feeglab.org-5Ftutorials-5F11-2D5FScripting-5Fcommand-2D5Fline-2D5Fstudy-2D5Ffunctions.html-2D23plotting-2D2Dmeasures-2526d-253DDwIGaQ-2526c-253D-2D35OiAkTchMrZOngvJPOeA-2526r-253DkB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE-2526m-253DzCZzq-5FwBqEWelhXHg4ghBGQxhsI5nrsj21I5XvAbfEw-2526s-253DfHR7S-5FE50Bt-5F7j1SYgG-5FGXVumlWP0DBLPFCl5m8Na9I-2526e-253D-26amp-3Bdata-3D04-257C01-257Cpaul.anthony.beach-2540emory.edu-257C0b722fc7e739448d784408d94b91e9cc-257Ce004fb9cb0a4424fbcd0322606d5df38-257C0-257C0-257C637623912335463478-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C2000-26amp-3Bsdata-3Dcdzkv-252FWiHMqfciIFWdoBTkOj-252FTzBBy0cgvjCSMvKDIc-253D-26amp-3Breserved-3D0&d=DwIGaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=1Rg8_2SDlukIFHUjJ7xZiB7EOiebyxrCtb3eLXqt-zA&s=74qAVtRmh7EUscGmhzRzccOOec7tYvd9YU0XR-PmkYw&e=  
>>>
>>> In scripts, the EEGLAB function “fillcurves" is also easy to use to create shaded areas.
>>> See the function help message for more details.
>>>
>>> figure; fillcurves(rand(1,100), rand(1,100)+1.5);
>>>
>>> Arno
>>>
>>> On Jul 18, 2021, at 11:51 PM, Cedric Cannard via eeglablist <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>> wrote:
>>>
>>> Hi Paul,
>>>
>>> Below is an example of one subject's epoched data. Define your channel_number of interest and for grand average. FOr you, the 3rd dimension is subjects instead of epochs.
>>>
>>> data1 = squeeze(EEG.data(channel_number,:,:));
>>> nEpochs = size(data1,2);
>>> data1_mean = mean(data1,2)';
>>> data1_se = std(data1 ./ sqrt(nEpochs),[],2)';
>>> color1 = [0, 0.4470, 0.7410];
>>> xAxis = 1:size(data1,1);        %ADJUST WITH YOUR LAGS
>>>
>>> plot(xAxis, data1_mean,'LineWidth',2,'Color',color1); hold on
>>> fillhandle = fill([xAxis fliplr(xAxis)], [data1_mean-data1_se fliplr(data1_mean+data1_se)], color1);
>>> set(fillhandle,'EdgeColor', color1,'FaceAlpha',0.2,'EdgeAlpha',0.8);
>>> set(gca,'FontSize',12,'layer','top');
>>> grid on; axis tight; box on;
>>> ylabel('ERP amplitude','FontSize',12);
>>> xlabel('Time','FontSize',12);
>>> hPlots = flip(findall(gcf,'Type','Line'));
>>> legend(hPlots, 'data1Name (SE)');
>>>
>>> And simply duplicate the lines containing data1 with data2 to superimpose another condition/group (i.e., data2).
>>>
>>> Cedric
>>>
>>>
>>> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
>>>
>>> On Sunday, July 18th, 2021 at 4:25 AM, Beach, Paul via eeglablist <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>> wrote:
>>>
>>> Hi EEGLAB’ers
>>>
>>> I’ve seen this posted a few times. Seems like it’s relatively standard now to include standard error “shades” in publications these days of ERP data. I’d like to do this on my grand averaged STUDY data but am having a few hard time figuring out how to do so in EEGLAB. I sawCedric
>>>
>>> had recommended a function he made using Matlab’s “fill” function, but seeing as this was seen in archived eeglablist data I cannot get the actual function.
>>>
>>> Does anyone have tips/tricks for doing this in EEGLAB or other (preferably simple) methods?
>>>
>>> Thanks!
>>>
>>> Paul
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>
>>> Paul Beach DO, PhD
>>>
>>> PGY6, Movement Disorder Fellow
>>>
>>> Department of Neurology
>>>
>>> Emory University School of Medicine
>>>
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>> -- 
>> Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
>> Neurobiology Research Unit,
>> Building 8057, Blegdamsvej 9
>> Copenhagen University Hospital, Rigshospitalet
>> DK-2100 Copenhagen, Denmark
>>
>> wamcyril at gmail.com
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cpernet.github.io_&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=Z7xZV5R_nUk8PVGqkl2HGJUdeipDuU0QmiPBEkN30Z4&s=sEAX8Z6_IU83KFXhPGKmCHxVzXDXFutPOw4BoYBdXYc&e= 
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>
-- 
Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
Neurobiology Research Unit,
Building 8057, Blegdamsvej 9
Copenhagen University Hospital, Rigshospitalet
DK-2100 Copenhagen, Denmark

wamcyril at gmail.com
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